Drug Discovery

The challenge in object-based visual reasoning lies in generating concept representations that are both descriptive and distinct. Achieving this in an unsupervised manner requires human users to understand the model's learned concepts and, if necessary, revise incorrect ones. To address this challenge, we introduce the Neural Concept Binder (NCB), a novel framework for deriving both discrete and continuous concept representations, which we refer to as "concept-slot encodings". NCB employs two types of binding: "soft binding", which leverages the recent SysBinder mechanism to obtain object-factor encodings, and subsequent "hard binding", achieved through hierarchical clustering and retrieval-based inference. This enables obtaining expressive, discrete representations from unlabeled images. Moreover, the structured nature of NCB's concept representations allows for intuitive inspection and the straightforward integration of external knowledge, such as human input or insights from other AI models like GPT-4. Additionally, we demonstrate that incorporating the hard binding mechanism preserves model performance while enabling seamless integration into both neural and symbolic modules for complex reasoning tasks. We validate the effectiveness of NCB through evaluations on our newly introduced CLEVR-Sudoku dataset.

Sequences of events, such as crashes in the stock market or outages in a network, contain strong temporal dependencies, whose understanding is crucial to react to and influence future events. In this paper, we study the problem of discovering the underlying causal structure from event sequences. To this end, we introduce a new causal model, where individual events of the cause trigger events of the effect with dynamic delays. We show that in contrast to existing methods based on Granger causality, our model is identifiable for both instant and delayed effects. We base our approach on the Algorithmic Markov Condition, by which we identify the true causal network as the one that minimizes the Kolmogorov complexity. As the Kolmogorov complexity is not computable, we instantiate our model using Minimum Description Length and show that the resulting score identifies the causal direction. To discover causal graphs, we introduce the Cascade algorithm, which adds edges in topological order. Extensive evaluation shows that Cascade outperforms existing methods in settings with instantaneous effects, noise, and multiple colliders, and discovers insightful causal graphs on real-world data.

Learning the unique directed acyclic graph corresponding to an unknown causal model is a challenging task. Methods based on functional causal models can identify a unique graph, but either suffer from the curse of dimensionality or impose strong parametric assumptions. To address these challenges, we propose a novel hybrid approach for global causal discovery in observational data that leverages local causal substructures. We first present a topological sorting algorithm that leverages ancestral relationships in linear structural causal models to establish a compact top-down hierarchical ordering, encoding more causal information than linear orderings produced by existing methods. We demonstrate that this approach generalizes to nonlinear settings with arbitrary noise. We then introduce a nonparametric constraint-based algorithm that prunes spurious edges by searching for local conditioning sets, achieving greater accuracy than current methods. We provide theoretical guarantees for correctness and worst-case polynomial time complexities, with empirical validation on synthetic data.

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation https://github.com/WillHua127/ReactZyme.

Exploiting symmetry inherent in data can significantly improve the sample efficiency of a learning procedure and the generalization of learned models. When data clearly reveals underlying symmetry, leveraging this symmetry can naturally inform the design of model architectures or learning strategies. Yet, in numerous real-world scenarios, identifying the specific symmetry within a given data distribution often proves ambiguous. To tackle this, some existing works learn symmetry in a data-driven manner, parameterizing and learning expected symmetry through data. However, these methods often rely on explicit knowledge, such as pre-defined Lie groups, which are typically restricted to linear or affine transformations. In this paper, we propose a novel symmetry learning algorithm based on transformations defined with one-parameter groups, continuously parameterized transformations flowing along the directions of vector fields called infinitesimal generators. Our method is built upon minimal inductive biases, encompassing not only commonly utilized symmetries rooted in Lie groups but also extending to symmetries derived from nonlinear generators. To learn these symmetries, we introduce a notion of a validity score that examine whether the transformed data is still valid for the given task. The validity score is designed to be fully differentiable and easily computable, enabling effective searches for transformations that achieve symmetries innate to the data. We apply our method mainly in two domains: image data and partial differential equations, and demonstrate its advantages. Our codes are available at \url{https://github.com/kogyeonghoon/learning-symmetry-from-scratch.git}.

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. % S-MolSearch processes both labeled and unlabeled data, trains molecular structural encoders, and generates soft labels for unlabeled data, drawing on the principles of inverse optimal transport. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

Revealing the underlying causal mechanisms in the real world is the key to the development of science. Despite the progress in the past decades, traditional causal discovery approaches (CDs) mainly rely on high-quality measured variables, usually given by human experts, to find causal relations. The lack of well-defined high-level variables in many real-world applications has already been a longstanding roadblock to a broader application of CDs. To this end, this paper presents Causal representatiOn AssistanT (COAT) that introduces large language models (LLMs) to bridge the gap. LLMs are trained on massive observations of the world and have demonstrated great capability in extracting key information from unstructured data. Therefore, it is natural to employ LLMs to assist with proposing useful high-level factors and crafting their measurements. Meanwhile, COAT also adopts CDs to find causal relations among the identified variables as well as to provide feedback to LLMs to iteratively refine the proposed factors. We show that LLMs and CDs are mutually beneficial and the constructed feedback provably also helps with the factor proposal. We construct and curate several synthetic and real-world benchmarks including analysis of human reviews and diagnosis of neuropathic and brain tumors, to comprehensively evaluate COAT. Extensive empirical results confirm the effectiveness and reliability of COAT with significant improvements.

Despite recent popularity of attention-based neural architectures in core AI fields like natural language processing (NLP) and computer vision (CV), their potential in modeling complex physical systems remains under-explored. Learning problems in physical systems are often characterized as discovering operators that map between function spaces based on a few instances of function pairs. This task frequently presents a severely ill-posed PDE inverse problem. In this work, we propose a novel neural operator architecture based on the attention mechanism, which we coin Nonlocal Attention Operator (NAO), and explore its capability towards developing a foundation physical model. In particular, we show that the attention mechanism is equivalent to a double integral operator that enables nonlocal interactions among spatial tokens, with a data-dependent kernel characterizing the inverse mapping from data to the hidden parameter field of the underlying operator. As such, the attention mechanism extracts global prior information from training data generated by multiple systems, and suggests the exploratory space in the form of a nonlinear kernel map. Consequently, NAO can address ill-posedness and rank deficiency in inverse PDE problems by encoding regularization and achieving generalizability. Lastly, we empirically demonstrate the advantages of NAO over baseline neural models in terms of the generalizability to unseen data resolutions and system states. Our work not only suggests a novel neural operator architecture for learning an interpretable foundation model of physical systems, but also offers a new perspective towards understanding the attention mechanism.

Causal knowledge about the relationships among decision variables and a reward variable in a bandit setting can accelerate the learning of an optimal decision. Current works often assume the causal graph is known, which may not always be available a priori. Motivated by this challenge, we focus on the causal bandit problem in scenarios where the underlying causal graph is unknown and may include latent confounders. While intervention on the parents of the reward node is optimal in the absence of latent confounders, this is not necessarily the case in general. Instead, one must consider a set of possibly optimal arms/interventions, each being a special subset of the ancestors of the reward node, making causal discovery beyond the parents of the reward node essential. For regret minimization, we identify that discovering the full causal structure is unnecessary; however, no existing work provides the necessary and sufficient components of the causal graph. We formally characterize the set of necessary and sufficient latent confounders one needs to detect or learn to ensure that all possibly optimal arms are identified correctly. We also propose a randomized algorithm for learning the causal graph with a limited number of samples, providing a sample complexity guarantee for any desired confidence level. In the causal bandit setup, we propose a two-stage approach. In the first stage, we learn the induced subgraph on ancestors of the reward, along with a necessary and sufficient subset of latent confounders, to construct the set of possibly optimal arms. We show that for our proposed algorithm, the number of intervention samples required to learn the set of possibly optimal arms scales polynomially with respect to the number of nodes. The second phase involves the application of a standard bandit algorithm, such as the UCB algorithm. We also establish a regret bound for our two-phase approach, which is sublinear in the number of rounds.

In this paper, we study a practical yet challenging task, On-the-fly Category Discovery (OCD), aiming to online discover the newly-coming stream data that belong to both known and unknown classes, by leveraging only known category knowledge contained in labeled data. Previous OCD methods employ the hash-based technique to represent old/new categories by hash codes for instance-wise inference. However, directly mapping features into low-dimensional hash space not only inevitably damages the ability to distinguish classes and but also causes ``high sensitivity'' issue, especially for fine-grained classes, leading to inferior performance. To address these drawbacks, we propose a novel Prototypical Hash Encoding (PHE) framework consisting of Category-aware Prototype Generation (CPG) and Discriminative Category Encoding (DCE) to mitigate the sensitivity of hash code while preserving rich discriminative information contained in high-dimension feature space, in a two-stage projection fashion. CPG enables the model to fully capture the intra-category diversity by representing each category with multiple prototypes. DCE boosts the discrimination ability of hash code with the guidance of the generated category prototypes and the constraint of minimum separation distance. By jointly optimizing CPG and DCE, we demonstrate that these two components are mutually beneficial towards an effective OCD. Extensive experiments show the significant superiority of our PHE over previous methods, e.g. obtaining an improvement of +5.3% in ALL ACC averaged on all datasets. Moreover, due to the nature of the interpretable prototypes, we visually analyze the underlying mechanism of how PHE helps group certain samples into either known or unknown categories. Code is available at https://github.com/HaiyangZheng/PHE.

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limitations in flexibility and scope. To address these challenges, avoid repetitive coding efforts, and ensure fair comparison of models, we introduce FlexMol, a comprehensive toolkit designed to facilitate the construction and evaluation of diverse model architectures across various datasets and performance metrics. FlexMol offers a robust suite of preset model components, including 16 drug encoders, 13 protein sequence encoders, 9 protein structure encoders, and 7 interaction layers. With its easy-to-use API and flexibility, FlexMol supports the dynamic construction of over 70, 000 distinct combinations of model architectures. Additionally, we provide detailed benchmark results and code examples to demonstrate FlexMol’s effectiveness in simplifying and standardizing MRL model development and comparison. FlexMol is open-sourced and available at https://github.com/Steven51516/FlexMol.

Symmetry detection has been shown to improve various machine learning tasks. In the context of continuous symmetry detection, current state of the art experiments are limited to the detection of affine transformations. Under the manifold assumption, we outline a framework for discovering continuous symmetry in data beyond the affine transformation group. We also provide a similar framework for discovering discrete symmetry. We experimentally compare our method to an existing method known as LieGAN and show that our method is competitive at detecting affine symmetries for large sample sizes and superior than LieGAN for small sample sizes. We also show our method is able to detect continuous symmetries beyond the affine group and is generally more computationally efficient than LieGAN.

Many causal discovery methods typically rely on the assumption of independent noise, yet real-life situations often involve deterministic relationships. In these cases, observed variables are represented as deterministic functions of their parental variables without noise. When determinism is present, constraint-based methods encounter challenges due to the violation of the faithfulness assumption. In this paper, we find, supported by both theoretical analysis and empirical evidence, that score-based methods with exact search can naturally address the issues of deterministic relations under rather mild assumptions. Nonetheless, exact score-based methods can be computationally expensive. To enhance the efficiency and scalability, we develop a novel framework for causal discovery that can detect and handle deterministic relations, called Determinism-aware Greedy Equivalent Search (DGES). DGES comprises three phases: (1) identify minimal deterministic clusters (i.e., a minimal set of variables with deterministic relationships), (2) run modified Greedy Equivalent Search (GES) to obtain an initial graph, and (3) perform exact search exclusively on the deterministic cluster and its neighbors. The proposed DGES accommodates both linear and nonlinear causal relationships, as well as both continuous and discrete data types. Furthermore, we investigate the identifiability conditions of DGES. We conducted extensive experiments on both simulated and real-world datasets to show the efficacy of our proposed method.

Causal interactions among a group of variables are often modeled by a single causal graph. In some domains, however, these interactions are best described by multiple co-existing causal graphs, e.g., in dynamical systems or genomics. This paper addresses the hitherto unknown role of interventions in learning causal interactions among variables governed by a mixture of causal systems, each modeled by one directed acyclic graph (DAG). Causal discovery from mixtures is fundamentally more challenging than single-DAG causal discovery. Two major difficulties stem from (i) an inherent uncertainty about the skeletons of the component DAGs that constitute the mixture and (ii) possibly cyclic relationships across these component DAGs. This paper addresses these challenges and aims to identify edges that exist in at least one component DAG of the mixture, referred to as the *true* edges. First, it establishes matching necessary and sufficient conditions on the size of interventions required to identify the true edges. Next, guided by the necessity results, an adaptive algorithm is designed that learns all true edges using ${\cal O}(n^2)$ interventions, where $n$ is the number of nodes. Remarkably, the size of the interventions is optimal if the underlying mixture model does not contain cycles across its components. More generally, the gap between the intervention size used by the algorithm and the optimal size is quantified. It is shown to be bounded by the *cyclic complexity number* of the mixture model, defined as the size of the minimal intervention that can break the cycles in the mixture, which is upper bounded by the number of cycles among the ancestors of a node.

What data or environments to use for training to improve downstream performance is a longstanding and very topical question in reinforcement learning. In particular, Unsupervised Environment Design (UED) methods have gained recent attention as their adaptive curricula promise to enable agents to be robust to in- and out-of-distribution tasks. This work investigates how existing UED methods select training environments, focusing on task prioritisation metrics. Surprisingly, despite methods aiming to maximise regret in theory, the practical approximations do not correlate with regret but with success rate. As a result, a significant portion of an agent's experience comes from environments it has already mastered, offering little to no contribution toward enhancing its abilities. Put differently, current methods fail to predict intuitive measures of *learnability*. Specifically, they are unable to consistently identify those scenarios that the agent can sometimes solve, but not always. Based on our analysis, we develop a method that directly trains on scenarios with high learnability. This simple and intuitive approach outperforms existing UED methods in several binary-outcome environments, including the standard domain of Minigrid and a novel setting closely inspired by a real-world robotics problem. We further introduce a new adversarial evaluation procedure for directly measuring robustness, closely mirroring the conditional value at risk (CVaR). We open-source all our code and present visualisations of final policies here: https://github.com/amacrutherford/sampling-for-learnability.

Unsupervised skill discovery carries the promise that an intelligent agent can learn reusable skills through autonomous, reward-free interactions with environments. Existing unsupervised skill discovery methods learn skills by encouraging distinguishable behaviors that cover diverse states. However, in complex environments with many state factors (e.g., household environments with many objects), learning skills that cover all possible states is impossible, and naively encouraging state diversity often leads to simple skills that are not ideal for solving downstream tasks. This work introduces Skill Discovery from Local Dependencies (SkiLD), which leverages state factorization as a natural inductive bias to guide the skill learning process. The key intuition guiding SkiLD is that skills that induce \textbf{diverse interactions} between state factors are often more valuable for solving downstream tasks. To this end, SkiLD develops a novel skill learning objective that explicitly encourages the mastering of skills that effectively induce different interactions within an environment. We evaluate SkiLD in several domains with challenging, long-horizon sparse reward tasks including a realistic simulated household robot domain, where SkiLD successfully learns skills with clear semantic meaning and shows superior performance compared to existing unsupervised reinforcement learning methods that only maximize state coverage.

Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries. However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult. In this paper we propose Reaction-GFlowNet (RGFN), an extension of the GFlowNet framework that operates directly in the space of chemical reactions, thereby allowing out-of-the-box synthesizability while maintaining comparable quality of generated candidates. We demonstrate that with the proposed set of reactions and building blocks, it is possible to obtain a search space of molecules orders of magnitude larger than existing screening libraries coupled with low cost of synthesis. We also show that the approach scales to very large fragment libraries, further increasing the number of potential molecules. We demonstrate the effectiveness of the proposed approach across a range of oracle models, including pretrained proxy models and GPU-accelerated docking.

Constantly discovering novel concepts is crucial in evolving environments. This paper explores the underexplored task of Continual Generalized Category Discovery (C-GCD), which aims to incrementally discover new classes from *unlabeled* data while maintaining the ability to recognize previously learned classes. Although several settings are proposed to study the C-GCD task, they have limitations that do not reflect real-world scenarios. We thus study a more practical C-GCD setting, which includes more new classes to be discovered over a longer period, without storing samples of past classes. In C-GCD, the model is initially trained on labeled data of known classes, followed by multiple incremental stages where the model is fed with unlabeled data containing both old and new classes. The core challenge involves two conflicting objectives: discover new classes and prevent forgetting old ones. We delve into the conflicts and identify that models are susceptible to *prediction bias* and *hardness bias*. To address these issues, we introduce a debiased learning framework, namely **Happy**, characterized by **H**ardness-**a**ware **p**rototype sampling and soft entro**py** regularization. For the *prediction bias*, we first introduce clustering-guided initialization to provide robust features. In addition, we propose soft entropy regularization to assign appropriate probabilities to new classes, which can significantly enhance the clustering performance of new classes. For the *harness bias*, we present the hardness-aware prototype sampling, which can effectively reduce the forgetting issue for previously seen classes, especially for difficult classes. Experimental results demonstrate our method proficiently manages the conflicts of C-GCD and achieves remarkable performance across various datasets, e.g., 7.5% overall gains on ImageNet-100. Our code is publicly available at https://github.com/mashijie1028/Happy-CGCD.

Fitness functions map large combinatorial spaces of biological sequences to properties of interest. Inferring these multimodal functions from experimental data is a central task in modern protein engineering. Global epistasis models are an effective and physically-grounded class of models for estimating fitness functions from observed data. These models assume that a sparse latent function is transformed by a monotonic nonlinearity to emit measurable fitness. Here we demonstrate that minimizing supervised contrastive loss functions, such as the Bradley-Terry loss, is a simple and flexible technique for extracting the sparse latent function implied by global epistasis. We argue by way of a fitness-epistasis uncertainty principle that the nonlinearities in global epistasis models can produce observed fitness functions that do not admit sparse representations, and thus may be inefficient to learn from observations when using a Mean Squared Error (MSE) loss (a common practice). We show that contrastive losses are able to accurately estimate a ranking function from limited data even in regimes where MSE is ineffective and validate the practical utility of this insight by demonstrating that contrastive loss functions result in consistently improved performance on empirical benchmark tasks.

When solving long-horizon tasks, it is intriguing to decompose the high-level task into subtasks. Decomposing experiences into reusable subtasks can improve data efficiency, accelerate policy generalization, and in general provide promising solutions to multi-task reinforcement learning and imitation learning problems. However, the concept of subtasks is not sufficiently understood and modeled yet, and existing works often overlook the true structure of the data generation process: subtasks are the results of a *selection* mechanism on actions, rather than possible underlying confounders or intermediates. Specifically, we provide a theory to identify, and experiments to verify the existence of selection variables in such data. These selections serve as subgoals that indicate subtasks and guide policy. In light of this idea, we develop a sequential non-negative matrix factorization (seq- NMF) method to learn these subgoals and extract meaningful behavior patterns as subtasks. Our empirical results on a challenging Kitchen environment demonstrate that the learned subtasks effectively enhance the generalization to new tasks in multi-task imitation learning scenarios. The codes are provided at this [*link*](https://anonymous.4open.science/r/Identifying\_Selections\_for\_Unsupervised\_Subtask\_Discovery/README.md).